Variant report

Variant	rs2930195
Chromosome Location	chr11:47993504-47993505
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 61 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs10769307	0.82[EUR][1000 genomes]
rs10838790	0.89[CEU][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes]
rs11039473	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11039480	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12099166	1.00[JPT][hapmap]
rs12270546	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12272781	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12273589	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1227997	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1227998	0.80[EUR][1000 genomes]
rs1227999	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1228000	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1228002	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1228004	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1228008	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1228018	0.90[CEU][hapmap];0.90[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.85[TSI][hapmap];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1228019	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1228020	1.00[ASW][hapmap];0.90[CEU][hapmap];0.90[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.87[TSI][hapmap];0.86[YRI][hapmap];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1228021	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1228022	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1228023	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12290628	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12294218	0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12295364	0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1681604	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1681627	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1681631	0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1681637	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1729281	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1729294	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1729297	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2626567	0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2697810	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2930188	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2930189	0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2950888	0.90[CEU][hapmap];0.90[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.91[MKK][hapmap];0.92[TSI][hapmap];0.82[EUR][1000 genomes]
rs4752886	0.82[EUR][1000 genomes]
rs6485797	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7104376	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7111419	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7113640	0.90[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes]
rs7116080	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7119280	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs73462871	1.00[ASN][1000 genomes]
rs73462874	1.00[ASN][1000 genomes]
rs73462875	1.00[ASN][1000 genomes]
rs7928153	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7932759	0.81[EUR][1000 genomes]
rs7941441	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs900699	0.90[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1052397	chr11:47675470-48594256	Weak transcription Strong transcription Genic enhancers Enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	97 gene(s)	inside rSNPs	diseases
2	nsv530620	chr11:47765455-48664555	Weak transcription Genic enhancers Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	93 gene(s)	inside rSNPs	diseases
3	nsv1036992	chr11:47794621-48666024	Strong transcription Flanking Active TSS Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
4	nsv897326	chr11:47891334-48035474	Flanking Bivalent TSS/Enh Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Active TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	nsv1036451	chr11:47902321-48616646	Weak transcription Enhancers ZNF genes & repeats Strong transcription Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
6	nsv541037	chr11:47902321-48616646	Enhancers Strong transcription Genic enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
7	nsv1047490	chr11:47916708-48388686	Enhancers Weak transcription Flanking Active TSS Strong transcription Bivalent/Poised TSS Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
8	nsv1044266	chr11:47929586-48276132	Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Strong transcription Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
9	nsv541038	chr11:47929586-48276132	Weak transcription Enhancers ZNF genes & repeats Strong transcription Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
10	nsv1053145	chr11:47967902-48086950	Enhancers Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
11	nsv870381	chr11:47989434-48142648	Enhancers Bivalent Enhancer Weak transcription Bivalent/Poised TSS Flanking Active TSS Strong transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2930195	NUP160	cis	cerebellum	SCAN

Chromatin state (count:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:47977000-47995400	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr11:47988600-47995400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
3	chr11:47989800-47994800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
4	chr11:47989800-47995200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr11:47990000-47994400	Weak transcription	Primary neutrophils fromperipheralblood	blood
6	chr11:47990000-47994800	Weak transcription	Osteobl	bone
7	chr11:47990000-47995000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
8	chr11:47990200-47995000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr11:47990200-47995000	Weak transcription	Primary monocytes fromperipheralblood	blood
10	chr11:47990200-47995000	Weak transcription	NHDF-Ad	bronchial
11	chr11:47990200-47995200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr11:47990400-47995200	Weak transcription	Monocytes-CD14+_RO01746	blood
13	chr11:47991200-47995200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
14	chr11:47991800-47995200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
15	chr11:47992400-47993600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr11:47993000-47993600	Enhancers	Cortex derived primary cultured neurospheres	brain
17	chr11:47993000-47993600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
18	chr11:47993000-47993800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr11:47993200-47993600	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr11:47993200-47993600	Enhancers	A549	lung
21	chr11:47993200-47994000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr11:47993400-47993600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
23	chr11:47993400-47993600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
24	chr11:47993400-47993600	Enhancers	NH-A	brain
25	chr11:47993400-47994800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
26	chr11:47993400-48001400	Weak transcription	Right Atrium	heart

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